OSX Notification Center Icon

You can force the Notification Center to refresh all of the icons by deleting the Notification Center database file (~/Library/Application Support/NotificationCenter/SOME_UUID.db) and then killing the Notification Center process (e.g., from Activity Monitor).

Unfortunately this has the side effect of deleting your notification history, but this wasn't too much of an issue for me.

I was able to fix this issue by incrementing the Build number in the General section for the build Target.